Dear Open Targets team and community,
I would like to use the L2G algorithm to investigate the genes associated with the loci of some newly generated summary statistics.
When I use the V2G annotation, I send a list of my lead SNPs to get the annotation via the API. However, I cannot find a way to load my sumstats or my loci in order to perform the L2G annotation in my disease of interest. Any guidance on how to do this would be greatly appreciated.
Thank you very much!
Unfortunately, it is currently not straightforward to run L2G on a new set of sumstats. The L2G github repository is available here, however, it would require your sumstats to be harmonised and fine-mapped in the same manner as the exisiting data in the portal, in addition, colocalisation analysis needs to be performed between your sumstats and various QTL datasets to generate the necessary input features for the L2G model.
We are in the process of re-vamping the genetics portal pipeline, and making the individual steps easily usable for the public is on our list of priorities.